##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##bcftoolsVersion=1.12+htslib-1.12
##bcftoolsCommand=mpileup --redo-BAQ --max-depth 0 --min-BQ 20 --min-MQ 20 --count-orphans --fasta-ref /home/priesgo/src/github/covigator-ngs-pipeline/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa --annotate AD ERR4145453.preprocessed.bam
##reference=file:///home/priesgo/src/github/covigator-ngs-pipeline/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa
##contig=<ID=MN908947.3,length=29903>
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (high-quality bases)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
##bcftools_callVersion=1.12+htslib-1.12
##bcftools_callCommand=call --multiallelic-caller --variants-only --ploidy 1; Date=Tue Oct 19 20:45:18 2021
##FILTER=<ID=LOW_FREQUENCY,Description="Set if true: INFO/IMF < 0.2">
##bcftools_filterVersion=1.12+htslib-1.12
##bcftools_filterCommand=filter --exclude 'INFO/IMF < 0.2' --soft-filter LOW_FREQUENCY -; Date=Tue Oct 19 20:45:21 2021
##FILTER=<ID=SUBCLONAL,Description="Set if true: INFO/IMF >= 0.2 && INFO/IMF < 0.8">
##bcftools_filterCommand=filter --exclude 'INFO/IMF >= 0.2 && INFO/IMF < 0.8' --soft-filter SUBCLONAL --output-type b -; Date=Tue Oct 19 20:45:21 2021
##INFO=<ID=OLD_CLUMPED,Number=1,Type=String,Description="Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX">
##bcftools_normVersion=1.12+htslib-1.12
##bcftools_normCommand=norm --multiallelics -any --check-ref e --fasta-ref /home/priesgo/src/github/covigator-ngs-pipeline/reference/Sars_cov_2.ASM985889v3.dna.toplevel.fa --old-rec-tag OLD_CLUMPED -; Date=Tue Oct 19 20:45:25 2021
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="ID for set of phased genotypes">
##bcftools_normCommand=norm --rm-dup exact -o ERR4145453.bcftools.normalized.vcf -; Date=Tue Oct 19 20:45:25 2021
##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -noStats -no-downstream -no-upstream -no-intergenic -no-intron -noShiftHgvs Sars_cov_2.ASM985889v3.101 ERR4145453.bcftools.normalized.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=CONS_HMM_SARS_COV_2,Number=1,Type=Float,Description="Mutation depletion score track based on significant enrichment/depletion of nonsingleton SARS-CoV-2 mutations (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateVersion=1.12+htslib-1.12
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_SARS_COV_2 --output-type z -; Date=Tue Oct 19 20:45:33 2021
##INFO=<ID=CONS_HMM_SARBECOVIRUS,Number=1,Type=Float,Description="30 ConsHMM conservation states learned from the Sarbecovirus sequence alignment (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionSarbecovirusConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionSarbecovirusConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_SARBECOVIRUS --output-type z -; Date=Tue Oct 19 20:45:33 2021
##INFO=<ID=CONS_HMM_VERTEBRATE_COV,Number=1,Type=Float,Description="30 ConsHMM conservation states learned from the vertebrate CoV sequence alignment (https://github.com/ernstlab/ConsHMM_CoV)">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionVertebrateCoVConsHMM.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/wuhCor1.mutDepletionVertebrateCoVConsHMM.header.txt -c CHROM,FROM,TO,CONS_HMM_VERTEBRATE_COV --output-type z -; Date=Tue Oct 19 20:45:33 2021
##INFO=<ID=PFAM_NAME,Number=.,Type=String,Description="Pfam domain name as reported in Ensembl annotations">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_names.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_names.header.txt -c CHROM,FROM,TO,PFAM_NAME --output-type z -; Date=Tue Oct 19 20:45:33 2021
##INFO=<ID=PFAM_DESCRIPTION,Number=.,Type=String,Description="Pfam domain description as reported in Ensembl annotations">
##bcftools_annotateCommand=annotate --annotations /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_descriptions.bed.gz --header-lines /home/priesgo/src/github/covigator-ngs-pipeline/reference/pfam_descriptions.header.txt -c CHROM,FROM,TO,PFAM_DESCRIPTION --output-type z -; Date=Tue Oct 19 20:45:33 2021
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	ERR4145453
MN908947.3	241	.	C	T	99.4152	PASS	DP=5;VDB=0.681156;SGB=-0.556411;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,3,1;MQ=60;CONS_HMM_SARS_COV_2=-1.25436;CONS_HMM_SARBECOVIRUS=-1.25436;CONS_HMM_VERTEBRATE_COV=0	GT:PL:AD	1:129,0:0,4
MN908947.3	3037	.	C	T	225.417	PASS	DP=94;VDB=0.027418;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,66,23;MQ=60;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.2772C>T|p.F924F|2772/21290|2772/21290|924/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=0;PFAM_NAME=NSP3_N_bCoV;PFAM_DESCRIPTION=Non-structural protein NSP3, N-terminal, betacoronavirus	GT:PL:AD	1:255,0:0,89
MN908947.3	14408	.	C	T	225.417	PASS	DP=75;VDB=0.309613;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,49,24;MQ=60;ANN=T|synonymous_variant|LOW|ORF1ab|gene-GU280_gp01|transcript|TRANSCRIPT_gene-GU280_gp01|protein_coding|1/1|c.14143C>T|p.L4715L|14143/21290|14143/21290|4715/7095||WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS;CONS_HMM_SARS_COV_2=0;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=-0.72839;PFAM_NAME=RNA_pol_N_coronovir;PFAM_DESCRIPTION=RNA polymerase, N-terminal, coronaviral	GT:PL:AD	1:255,0:0,73
MN908947.3	21784	.	T	G	228.37	PASS	DP=81;VDB=0.845817;SGB=-0.693147;RPB=0.789474;MQB=0.986842;MQSB=0.990551;BQB=0.973684;MQ0F=0;AC=1;AN=1;DP4=2,0,50,26;MQ=59;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.222T>G|p.N74K|222/3822|222/3822|74/1273||;CONS_HMM_SARS_COV_2=-0.80744;CONS_HMM_SARBECOVIRUS=0;CONS_HMM_VERTEBRATE_COV=-0.80744;PFAM_NAME=bCoV_S1_N;PFAM_DESCRIPTION=Betacoronavirus-like spike glycoprotein S1, N-terminal	GT:PL:AD	1:255,0:2,76
MN908947.3	23403	.	A	G	225.417	PASS	DP=137;VDB=0.648575;SGB=-0.693147;MQSB=1;MQ0F=0;AC=1;AN=1;DP4=0,0,109,23;MQ=60;ANN=G|missense_variant|MODERATE|S|gene-GU280_gp02|transcript|TRANSCRIPT_gene-GU280_gp02|protein_coding|1/1|c.1841A>G|p.D614G|1841/3822|1841/3822|614/1273||;CONS_HMM_SARS_COV_2=0.57215;CONS_HMM_SARBECOVIRUS=0.57215;CONS_HMM_VERTEBRATE_COV=0	GT:PL:AD	1:255,0:0,132